public class CompareSAMs extends CommandLineProgram
| Modifier and Type | Field | Description |
|---|---|---|
List<File> |
samFiles |
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY| Constructor | Description |
|---|---|
CompareSAMs() |
| Modifier and Type | Method | Description |
|---|---|---|
boolean |
areEqual() |
|
protected int |
doWork() |
Do the work after command line has been parsed.
|
int |
getMappingsDiffer() |
|
int |
getMappingsMatch() |
|
int |
getMissingLeft() |
|
int |
getMissingRight() |
|
int |
getUnmappedBoth() |
|
int |
getUnmappedLeft() |
|
int |
getUnmappedRight() |
|
static void |
main(String[] argv) |
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders@PositionalArguments(minElements=2, maxElements=2) public List<File> samFiles
public static void main(String[] argv)
protected int doWork()
doWork in class CommandLineProgrampublic int getMappingsMatch()
public int getUnmappedBoth()
public int getUnmappedLeft()
public int getUnmappedRight()
public int getMappingsDiffer()
public int getMissingLeft()
public int getMissingRight()
public boolean areEqual()